Computer-aided drug design (CADD) is one of the pivotal approaches to contemporary pre-
clinical drug discovery, and various computational techniques and software programs are …

Highlights•Providing concepts and generation processes of chemical fingerprints.•
Comparing the algorithms and characteristics among different types of fingerprints.• …

Motivation: Most bioactive molecules perform their action by interacting with proteins or other
macromolecules. However, for a significant fraction of them, the primary target remains …

Molecular similarity is a key concept in drug discovery. It is based on the assumption that
structurally similar molecules frequently have similar properties. Assessment of similarity …

In his philosophic musings “Meditations” the Emperor Marcus Aurelius asks “This thing, what
is it in itself, in its own constitution? What is its substance and material? And what its causal …

Natural products are continually explored in the development of new bioactive compounds
with industrial applications, attracting the attention of scientific research efforts due to their …

Polypharmacology, which focuses on designing therapeutics to target multiple receptors,
has emerged as a new paradigm in drug discovery. Polypharmacological effects are an …

We developed a novel approach called SHAFTS (SHA pe-F ea T ure S imilarity) for 3D
molecular similarity calculation and ligand-based virtual screening. SHAFTS adopts a hybrid …

In this article, we introduce Tsinghua Global Minimum (TGMin) as a new program for the
global minimum searching of geometric structures of gas-phase or surface-supported atomic …

We discuss how data unbiasing and simple methods such as protein-ligand Interaction
FingerPrint (IFP) can overestimate virtual screening performance. We also show that IFP is …